Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “bacterial isolates”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The Impact of Carotenoid Energy Levels on the Exciton Dynamics and Singlet–Triplet Annihilation in Isolated Bacterial Light-Harvesting 2 Complexes

The light-harvesting 2 (LH2) complex of purple phototrophic bacteria plays a critical role in absorbing solar energy and distributing the excitation energy. Exciton dynamics within LH2 complexes are controlled by the structural arrangement and energy levels of the bacteriochlorophyll (BChl) and carotenoid (Car) pigments. However, there is still debate over the competing light-harvesting versus energy-dissipation pathways. In this work, we compared five variants of the LH2 complex from genetically modified strains of Rhodobacter sphaeroides, all containing the same BChls but different Cars with increasing conjugation: zeta-carotene (N = 7; LH2 Zeta ), neurosporene (N = 9; LH2 Neu ), spheroidene (N = 10; LH2 Spher ), lycopene (N = 11; LH2 Lyco ), and spirilloxanthin (N = 13; LH2 Spir ). Absorption measurements confirmed that the Car excited-state energy decreased with increasing conjugation. Similarly, fluorescence spectra showed that the B850 BChl emission peak had an increasing red shift from LH2 Zeta →(LH2 Neu /LH2 Spher )→LH2 Lyco →LH2 Spir . In contrast, time-resolved fluorescence and ultrafast transient absorption (fs-TA) revealed similar excited-state lifetimes (∼1 ns) for all complexes except LH2 Spir (∼0.7 ns). From fs-TA analysis, an additional ∼7 ps nonradiative dissipation step from B850 BChl was observed for LH2 Zeta . Further, singlet− singlet and singlet−triplet annihilation studies showed a ∼50% average fluorescence lifetime reduction in LH2Zeta at high laser power and high repetition rate, compared to ∼10−15% reductions in LH2 Neu /LH2 Spher /LH2 Lyco and minimal lifetime change in LH2 Spir . In LH2 Zeta , the fastest decay component (<50 ps) became prominent at high repetition rates, consistent with strong singlet−triplet annihilation. Nanosecond TA measurements revealed long-lived (>40 μs) BChl triplet states in LH2 Zeta and signs of damage caused by singlet oxygen, whereas other LH2s showed faster triplet quenching (∼18 ns) by Cars. These findings highlight a key design principle of LH2 complexes: the Car triplet energy must be significantly lower than the BChl triplet energy to efficiently quench BChl triplets that otherwise act as potent “trap states,” causing exciton annihilation in laser-based experiments or photodamage in native membranes.

Absorption↗
DOE OSTI2026

Draft Genome Sequences of 14 Bacterial Isolates from the Rhizosphere of Bioenergy Sorghum

We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.

Black, Grace S.↗
DOE OSTI2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

Analytical Methods↗
DOE OSTI2026

Bacterial Bioleaching and Biorecovery for Biomining Unconventional Rare Earth Element Feedstocks

Bacterial metabolic interactions with rare earth elements (REEs) can be harnessed for biomining unconventional feedstocks like abandoned coal-mine drainage (AMD). Pennsylvania has ~500 AMD passive remediation systems that can precipitate REE rich solids. REEs include yttrium and the lanthanide series that are used in modern energy and technology. Bacteria that metabolically interact with REEs can be used for biomining in an affordable efficient process that does not require hazardous chemical additives. Currently, the microbial metal mechanisms that contribute to REE biorelease and biorecovery are poorly understood. Our work shows acidogenic bacterial isolates (Bacillus mycoides JR07 and Bacillus pseudomycoides KB7) successfully bioleach a mixed REE solution from AMD solids by their organic acid production and biofilm formation. Further, our work shows the potential for bacterial lanthanide-dependent enzymes to recover lanthanides from a mixed REE solution; here we have bacterial isolate Methylobacterium sp. B3 that can recover soluble lanthanum. Whole genome sequencing of Methylobacterium sp. B3 predict lanthanide-dependent methanol dehydrogenase XoxF. Understanding the microbial metabolism and genes involved in the REE release and recovery is crucial to optimize the biomining of AMD solids. Our work addresses the growing need to develop novel REE mining methods from unconventional feedstocks.

biogeochemistry↗
DOE OSTI2026

Populus_CSource_Screen

This dataset contains binary carbon-source growth results for bacterial isolates associated with Populus roots. The isolates are part of the Populus culture collection described by Carper et al. (2021), Cultivating the Bacterial Microbiota of Populus Roots (https://doi.org/10.1128/msystems.01306-20).

bacterial isolates↗
DOE OSTI2025

Five PMI Isolates from Populus Deltoides and Populus Trichocarpa

Five bacterial isolates were isolated from the roots of poplar trees (Populus deltoides and P. trichocarpa), which are model organisms and a main focus of the Plant-Microbe Interfaces (PMI) project at ORNL. These strains belong to genera are not well represented and give a more complete view of the microbial community and bacterial interactions with poplar trees. These strains will support future studies and contribute to the broader PMI goal of understanding microbe-microbe and plant-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbial Biomining for the Release and Recovery of Rare Earth Elements in Abandoned Coal Mine Drainage

Microbes can be used for biomining rare earth elements (REEs) from abandoned coal-mine drainage (AMD) solids. Domestically Pennsylvania has ~11,000 abandoned mines, with ~500 AMD passive remediation systems (PRSs) that precipitate REE rich solids. In passive systems, REEs, co-precipitate with manganese (Mn), accumulating as a valuable leachate when resolubilized. REEs like lanthanum (La) are used in battery technology. Microbial metabolism that co-resolubilize Mn and REEs could result in an affordable release process that does not require the addition of hazardous chemical additives. Microbial sequestering of La can be used for selective purification from a mixed REE composition. Currently, the microbial mechanisms that contribute to mass REE resolubilization and selective sequestration are poorly understood. We have isolated bacteria (Bacillus mycoides JR07 and Bacillus pseudomycoides KB7) that solubilize Mn oxide, La oxide, and AMD solids by acidogenesis. Preliminary results show methylotrophic bacterial isolate B3 can take up soluble La, which may have a potential application in the purification of La from a mixed REE leachate. Determining the microbial metabolism and genes involved in the REE resolubilization and selective biomining of La is crucial to optimize the biomining of AMD solids. Our work addresses the growing need to develop novel REE recovery methods from domestic sources.

microbiology↗
DOE OSTI2025

Spatially structured bacterial interactions alter algal carbon flow to bacteria

Phytoplankton account for nearly half of global photosynthetic carbon fixation, and the fate of that carbon is regulated in large part by microbial food web processing. We currently lack a mechanistic understanding of how interactions among heterotrophic bacteria impact the fate of photosynthetically fixed carbon. Here, we used a set of bacterial isolates capable of growing on exudates from the diatom Phaeodactylum tricornutum to investigate how bacteria-bacteria interactions affect the balance between exudate remineralization and incorporation into biomass. With exometabolomics and genome-scale metabolic modeling, we estimated the degree of resource competition between bacterial pairs. In a sequential spent media experiment, we found that pairwise interactions were more beneficial than predicted based on resource competition alone, and 30% exhibited facilitative interactions. To link this to carbon fate, we used single-cell isotope tracing in a custom cultivation system to compare the impact of different "primary" bacterial strains in close proximity to live P. tricornutum on a distal "secondary" strain. We found that a primary strain with a high degree of competition decreased secondary strain carbon drawdown by 51% at the single-cell level, providing a quantitative metric for the "cost" of competition on algal carbon fate. Additionally, a primary strain classified as facilitative based on sequential interactions increased total algal-derived carbon assimilation by 7.6 times, integrated over all members, compared to the competitive primary strain. Our findings suggest that the degree of interaction between bacteria along a spectrum from competitive to facilitative is directly linked to algal carbon drawdown.

genome-scale metabolic model↗
DOE OSTI2025

Unraveling the influence of microbial necromass on subsurface microbiomes: metabolite utilization and community dynamics

The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. It is currently unclear whether necromass metabolites from various microbes are different, whether certain groups of metabolites are preferentially utilized over others, or whether different microbial species respond to various necromass metabolites. In this study, we aimed to fill these knowledge gaps by designing enrichments with necromass as the sole nutrient source for subsurface microbial communities. We used the soluble fraction of necromass from bacterial isolates belonging to Arthrobacter, Agrobacterium, and Pseudomonas genera, and our results indicate that metabolite composition of necromass varied slightly across different strains but generally included amino acids, organic acids, and nucleic acid constituents. Arthrobacter-derived necromass appeared more recalcitrant. Necromass metabolites enriched diverse microbial genera, particularly Massilia sp. responded quickly regardless of the necromass source. Despite differences in necromass utilization, microbial community composition converged rapidly over time across the three different necromass amendments. Uracil, xanthine, valine, and phosphate-containing isomers were generally depleted over time, indicating microbial assimilation for maintenance and growth. However, numerous easily assimilable metabolites were not significantly depleted, suggesting efficient necromass recycling and the potential for necromass stabilization in systems. This study highlights the dynamic interactions between microbial necromass metabolites and subsurface microbial communities, revealing both selective utilization and rapid community and necromass convergence regardless of the necromass source.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Emergence and disruption of cooperativity in a denitrifying microbial community

Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N 2 O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N 2 O. Microbial denitrification is a primary contributor to biotic production of N 2 O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification within microbial communities. We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11. We have discovered that these two bacterial isolates, from a heavily nitrate (NO 3 − ) contaminated superfund site, complete denitrification through the exchange of nitrite (NO 2 − ) and nitric oxide (NO). The process partitioning of denitrification and other processes, including amino acid metabolism, contribute to increased cooperativity within this denitrifying community. We demonstrate that certain contexts, such as high NO 3 − , cause unbalanced growth of community members, due to differences in their substrate utilization kinetics. The altered growth characteristics of community members drives accumulation of toxic NO 2 − , which disrupts denitrification causing N 2 O off gassing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Imaging and analysis data of short-term co-culture in soilchip

Fluorescently tagged bacterial soil isolates were cultured with N-acetylglucosamine, chitopentose, or chitin in porous SoilChip devices designed to mimic the structural habitats found in soil. Imaging analysis was used to examine how microbial traits, nutrient substrate solubility and degree of polymerization, and time affected microbial growth and species’ spatial assembly.

Feng, Song [Pacific Northwest National Laboratory ↗
DOE OSTI2025

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change. IMPORTANCE Anthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

Choudoir, Mallory J. (ORCID:0000000291175150)↗
DOE OSTI2025

Bacterial Biomining Rare Earth Elements in Abandoned Coal Mine Drainage: Solubilization and Sequestration

Bacteria can be used to biomine rare earth elements (REEs) domestically from abandoned coal-mine drainage (AMD) solids. Pennsylvania has ~11,000 abandoned mines, with ~500 AMD passive remediation systems that precipitate AMD REE rich solids onsite. In passive systems, REEs, co-precipitate with manganese (Mn), accumulating as solids that can produce a valuable leachate when resolubilized. REEs like lanthanum (La) are used in battery technology. Microbial metabolic changes that co-resolubilize Mn and REEs could result in an affordable release process that does not require chemical additives and the select sequestering of REEs like La allow for the selective purification from a mixed REE composition. Currently, the microbial mechanisms that contribute to mass REE resolubilization and selective sequestration are poorly understood. We have isolated bacteria (Bacillus mycoides JR07 and Bacillus pseudomycoides KB7) that solubilize Mn oxide, La oxide, and AMD solids by acidogenesis. We have determined that isolates JR07 and KB7 solubilize the La from AMD PRS solids by their production of organic acids. Preliminary results show methylotrophic bacterial isolate B3 can take up soluble La(III), giving an avenue to purification of La from a rich REE leachate. Determining the microbial metabolism and genes involved in the mass resolubilization of REEs and selective biomining of La(III) is crucial to optimize the biomining of AMD solids. Our work addresses the growing need to develop novel REE recovery methods from domestic sources.

microbiology↗
DOE OSTI2024

Enhancement on selenium volatilization for phytoremediation: role of plant and soil microbe interaction

This study aimed at quantifying the potential effects of plant and soil microbial interaction on selenium (Se) volatilization, with the specific objectives of identifying soil bacteria associated with rabbitfoot grass (Polypogon monspeliensis) and demonstrating the enhancement of Se volatilization in the soil-Indian mustard (Brassica juncea) system through inoculation of the soil with the identified best Se-volatilizing bacterial strain. Soil bacteria were isolated from topsoil and rhizosphere soils of rabbitfoot grass, and the bacterial colonies were characterized via PCR-DGGE and DGGE band analysis prior to their identification using 16S rDNA sequencing technique.Bacillus cereusproduced over 500-fold more volatile Se in a culture medium treated with 15 µg Se/mL (equal mixture of SeO 4 2- , SeO 3 2- and selenomethionine) than any of the other eight identified bacterial strains. Inoculation of Indian mustard vegetated soil with the best Se volatilizing bacterial strainB. cereusresulted in a significant (p<0.05) increase in Se volatilization during a 7-day time period, compared to the soil-plant system without inoculation ofB. cereus. Thus, inoculation of the soil withB. cereussubstantially enhanced Se removal via biogenic volatilization in the soil-Indian mustard system. This study evaluated the role ofB. cereusin enhancing Se volatilization in soil-plant systems, and demonstrated the importance of plant and soil microbial interaction for Se phytoremediation.

Plant Sciences↗
DOE OSTI2026

HtPIP: High-throughput phage isolation platform increases diversity and reduces isolation time using multiple bacteria

Bacteriophages are ubiquitous in nature, but relatively few have been isolated and characterized compared to the number of bacterial strains. Phage biotechnology applications benefit from a diverse library of isolated phages to kill or transfer genetic material to a bacterium of interest. However, scaling up phage discovery for diverse bacterial hosts can be time-consuming and costly. Here, we developed an approach to capture novel phages for multiple bacterial strains in parallel from an environmental sample using commercially available 0.2-μM filter plates. Using this High-throughput Phage Isolation Platform (HtPIP), 12 novel phages were isolated spanning 9 diverse bacterial host genera. Eleven of the isolated phages define new phage species, with nine also defining new genera. The HtPIP was used to discover both DNA and RNA phages, including a Tectiviridae infecting Pseudomonas putida mt-2 and a Leviviricetes infecting a Microbacterium isolate, which represents the first cultured RNA phage infecting a host outside of Proteobacteria. Using a metagenomic approach, we demonstrate that the HtPIP captures a higher proportion of novel phages compared to traditional low-throughput methods.

High-throughput↗
DOE OSTI2025

Climate history modulates stress responses of common soil bacteria under experimental drought

Soil drying challenges microbial viability and survival, with bacteria employing various mechanisms to respond to shifts in osmolarity, including dormancy or metabolic upregulation of osmoprotectants. However, the extent to which these responses are shaped by an organism's phylogeny, or the climate history of a given environment is poorly understood. This study examines the responses of phylogenetically similar bacteria from semi-arid and humid tropical forest soils to osmotic and matric stress using synchrotron radiation-based Fourier Transform Infrared spectromicroscopy. This non-destructive approach depicts the biochemical phenotype for whole cells under control and stress conditions. We observed that, under osmotic stress, bacteria upregulated cell-signaling pathways, rapidly turned over lipid-storage compounds, and increased osmolyte production. In contrast, matric stress induced a more muted response, typically elevating the production of carbohydrate stress compounds, such as glycine betaine and trehalose. Whereas phylogenetically similar bacteria showed comparable biochemistry under control conditions, climate history played an important role in regulating responses to stress, whereby a stronger metabolic response was observed from semi-arid relative to tropical forest isolates. We conclude that bacterial stress response to drought can be more diverse than previously observed and regulated by both phylogeny and climate history.

54 ENVIRONMENTAL SCIENCES↗